This is the introduction to a 3-part Q&A with a panel of liquid biopsy experts addressing some of the issues faced in developing and deploying NGS-based liquid biopsy assays for clinical applications in oncology.
In this 3-part blog series, we will share highlights from a recent Liquid Biopsy Expert Panel webinar sponsored by LGC Seracare and facilitated by GenomeWeb, which brought together academic research and clinical experts in liquid biopsy technologies to discuss the benefits, shortcomings, challenges and recommendations for liquid biopsy adoption in the context of cancer disease management. The webinar drew a lot of interest and sparked in-depth questions from attendees, which required a post webinar follow-up response from all 3 panelists.
The 3 Panelists featured in this 3-part blog are:
Sandi Deans, PhD, Director, Genomics Quality Assessment (GenQA), UK
Ed Schuuring, PhD, Professor of Pathology and Medical Biology, University of Groningen, The Netherlands
Claudia Vollbrecht, PhD, Deputy Head of Molecular Pathology, Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
The idea of ctDNA testing using NGS has come a long way since its inception over 8 years ago, with two recent FDA approvals of cfDNA-based NGS tests as companion diagnostics. Before liquid biopsy can gain wide adoption within clinical practice, it will require rigorous pre-analytical, analytical and clinical validation that will culminate in a regulated use with clinical guidelines for application and adoption. Part of this exercise will be achieved using bespoke, fit-for-purpose cfDNA-based reference materials manufactured under cGMP and ISO 13485 designated facilities, offered by global organizations such as LGC Seracare. Such highly multiplexed and very “patient-like” liquid biopsy reference materials will support laboratories pre-analytical and analytical validation efforts, and help accelerate the clinical adoption and approvals to establish legitimacy of test results across labs and platforms.
A Joint Consensus of the Analytical Variables Group within the BloodPAC Consortium1 recommended the use of both clinical and contrived reference samples in ccfDNA-based NGS assay protocols to establish validation of different analytical variables. Contrived samples mimicking native circulating cell-free DNA (ccfDNA) have the advantage of being analyzed routinely to detect sources of liquid biopsy assay workflow errors and in monitoring assay performance. As previously described on the Diagnostic Precision blog, the utility of contrived ctDNA reference materials was demonstrated by a recent multi-laboratory study.
The application of plasma samples bearing circulating tumor DNA (ctDNA) as a surrogate for solid tumor biopsy is an area of significant research and clinical interest. Genomic aberrations associated with ctDNA have been shown to mirror the solid tumor mutational landscape and have the potential for early diagnosis of cancer as well as monitoring and tracking biomarkers associated with residual disease and recurrence/relapse. Despite this promise, there are still open questions regarding the best way to implement liquid biopsy approaches in the clinical setting.
The importance of rigorous validation when analyzing ctDNA was emphasized by all speakers as the approach poses numerous challenges:
- Low and variable ctDNA abundance in blood. In most cases, ctDNA accounts for a small fraction of total cell-free DNA (cfDNA) since most cfDNA is derived from blood cells. In early-stage cancer patients, ctDNA fraction can be lower than 0.1% as opposed to a typical tumor DNA fraction of 10% or more in a tissue biopsy sample.
- Complex workflows with many pre-analytical and analytical variables affecting the results.
- Ongoing need for the standardization and harmonization of assay performance requirements and reporting in clinical ctDNA testing.
We will present the responses to the myriad of questions posed by webinar attendees and the response from the expert panelists in a 3-part blog post. It is our hope that these Q&A exercise help the community in addressing the challenges and recommendations for developing and deploying NGS-based liquid biopsy assays for clinical applications in oncology.
Download the video to replay or watch the webinar The Promise of Liquid Biopsy for Cancer Diagnostics and Therapeutic Monitoring: Are We There Yet?
- Godsey, James H, et. al. “Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC's Analytical Variables Working Group.” Clinical chemistry, vol. 66,9 (2020): 1156-1166. https://doi.org/10.1093/clinchem/hvaa164.